Reserve the first level headings (#) for the start of a new Module. This will help to organize your portfolio in an intuitive fashion.
Note: Please edit this template to your heart’s content. This is meant to be the armature upon which you build your individual portfolio. You do not need to keep this instructive text in your final portfolio, although you do need to keep module and assignment names so we can identify what is what.
The first of your second level headers (##) is to be used for the portfolio content checks. The Module 01 portfolio check has been built for you directly into this template, but will also be available as a stand-alone markdown document available on the MICB425 GitHub so that you know what is required in each module section in your portfolio. The completion status and comments will be filled in by the instructors during portfolio checks when your current portfolios are pulled from GitHub.
The remaining second level headers (##) are for separating data science Friday, regular course, and project content. In this module, you will only need to include data science Friday and regular course content; projects will come later in the course.
Third level headers (###) should be used for links to assignments, evidence worksheets, problem sets, and readings, as seen here.
Use this space to include your installation screenshots.
Detail the code you used to create, initialize, and push your portfolio repo to GitHub. This will be helpful as you will need to repeat many of these steps to update your porfolio throughout the course.
git config –global user.name “Jonah Lin”
git config – global user.email “1jonahlin1@gmail.com”
… Set up MICB425_Materials folder in relevant place …
mkdir MICB425_Portfolio
cd MICB425_Portfolio
git init
git add .
git commit -m “State commit message here”
git remote add origin git@github.com:IStrykerI/MICB425_Portfolio.git
git remote -v
git push -u origin master
… Needed key to get to this repo since it’s locked. Regular submit codes below …
git add .
git commit -m “State commit message here”
git push
Paste your code from the in-class activity of recreating the example PDF.
The following assignment is an exercise for the reproduction of this .html document using the RStudio and RMarkdown tools we’ve shown you in class. Hopefully by the end of this, you won’t feel at all the way this poor PhD student does. We’re here to help, and when it comes to R, the internet is a really valuable resource. This open-source program has all kinds of tutorials online.
http://phdcomics.com/ Comic posted 2-12-2018
The goal of this R Markdown html challenge is to give you an opportunity to play with a bunch of different RMarkdown formatting. Consider it a chance to flex your RMarkdown muscles. Your goal is to write your own RMarkdown that rebuilds this html document as close to the original as possible. So, yes, this means you get to copy my irreverant tone exactly in your own Markdowns. It’s a little window into my psyche. Enjoy =)
Hint: Go to the PhD Comics Website to see if you can find the image above.
If you can’t find that exact image, just find a comparable image from the PhD Comics website and include it in your markdown.
Let’s be honest, this header is a little arbitrary. But show me that you can reproduce headers with different levels please. This is a level 3 header, for your reference (You can most easily tell this from the table of contents).
Perhaps you’re already really confused by the whole markdown thing. Maybe you’re so confused that you’ve forgotton how to add. Never fear! A calculator R is here:
1231521+12341556280987
## [1] 1.234156e+13
Or maybe, after you’ve added those numbers, you feel like it’s about time for a table!
I’m going to leave all the guts of the coding here so you can see how libraries (R packages) are loaded into R (More on that later). It’s not terribly pretty, but it hints at how R works and how you will use it in the future. The summary function used below is a nice data exploration function that you may use in thefuture.
library(knitr)
kable(summary(cars),caption="I made this table with kable in the knitr package library")
| speed | dist | |
|---|---|---|
| Min. : 4.0 | Min. : 2.00 | |
| 1st Qu.:12.0 | 1st Qu.: 26.00 | |
| Median :15.0 | Median : 36.00 | |
| Mean :15.4 | Mean : 42.98 | |
| 3rd Qu.:19.0 | 3rd Qu.: 56.00 | |
| Max. :25.0 | Max. :120.00 |
And now you’ve almost finished your first RMarkdown! Feeling excited? We are! In fact, we’re so excited that maybe we need a big finale eh? Here’s ours! Include a fun GIF of your choice!
The template for the first Evidence Worksheet has been included here. The first thing for any assignment should link(s) to any relevant literature (which should be included as full citations in a module references section below).
You can copy-paste in the answers you recorded when working through the evidence worksheet into this portfolio template.
As you include Evidence worksheets and Problem sets in the future, ensure that you delineate Questions/Learning Objectives/etc. by using headers that are 4th level and greater. This will still create header markings when you render (knit) the document, but will exclude these levels from the Table of Contents. That’s a good thing. You don’t’ want to clutter the Table of Contents too much.
Describe the numerical abundance of microbial life in relation to ecology and biogeochemistry of Earth systems.
What were the primary methodological approaches used?
Primary Methodological Approaches: Usage of various papers for estimating the number of prokaryotes in various habitats, total C content (Mainly), turnover times, and cellular production rates
Comment on the emergence of microbial life and the evolution of Earth systems
Indicate the key events in the evolution of Earth systems at each approximate moment in the time series. If times need to be adjusted or added to the timeline to fully account for the development of Earth systems, please do so.
Describe the dominant physical and chemical characteristics of Earth systems at the following waypoints:
Describe the numerical abundance of microbial life in relation to the ecology and biogeochemistry of Earth systems.
What are the primary prokaryotic habitats on Earth and how do they vary with respect to their capacity to support life? Provide a breakdown of total cell abundance for each primary habitat from the tables provided in the text.
Primary Prokaryotic Habitats on Earth:How do they vary with respect to their capacity to support life:
Aquatic environments have the highest rate of cellular productivity while subsurface environments have the lowest rate of cellular productivity between the 3 habitats (Even though they have the highest population).
What is the estimated prokaryotic cell abundance in the upper 200 m of the ocean and what fraction of this biomass is represented by marine cyanobacterium including Prochlorococcus? What is the significance of this ratio with respect to carbon cycling in the ocean and the atmospheric composition of the Earth?
Estimated Prokaryotic Cell Abundance in Upper 200m of Ocean: 3.6 * 1028
Fraction represented by marine cyanobacterium (+ Prochlorococcus): (4 * 104) / (5 * 105) * 100 = 8%
Significance of this ratio with respect to C cycling in ocean and atmospheric composition of Earth:
Approx. 8% of these prokaryotes (Cyanobacteria + Prochlorococcus) are contributing to the conversion of CO2 to O2
What is the difference between an autotroph, heterotroph, and a lithotroph based on information provided in the text?
Difference Between Autotroph/Heterotroph/Lithotroph:Based on information provided in text.
Based on information provided in the text and your knowledge of geography what is the deepest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this depth?
Deepest Habitat: 4 km (Terrestrial) and 10.9 - 14.9 km (Marine)
Primary Limiting Factor: Temperature (125oC)
Based on information provided in the text your knowledge of geography what is the highest habitat capable of supporting prokaryotic life? What is the primary limiting factor at this height?
Highest Habitat: 77 km (In reality ~20 km above surface)
Primary Limiting Factor(s): Stable Space/Resources/Radiation/Lack of Moisture
Based on estimates of prokaryotic habitat limitation, what is the vertical distance of the Earth’s biosphere measured in km?
Vertical Distance of Earth’s Biosphere: ~24 - 44 km
How was annual cellular production of prokaryotes described in Table 7 column four determined? (Provide an example of the calculation)
Annual Cellular Production of Prokaryotes:
Population * (Turnover/Yr) = Cells/Yr
3.6 * 1028 * 365 Days/16 Turnovers = 8.2 * 1029 Cells/Yr
What is the relationship between carbon content, carbon assimilation efficiency and turnover rates in the upper 200m of the ocean? Why does this vary with depth in the ocean and between terrestrial and marine habitats?
Relationship between C content, C assimilation efficiency, and turnover rates in the upper 200m of ocean:
Due to the high turnover rates in the upper 200m of ocean and the estimated low C assimilation efficiency (0.2), the C content will be low since the majority of C will be used to support the turnover of prokaryotes and not assimilated.
This varies with depth in ocean and between terrestrial and marine habitats because as the depth increases, the turnover rate decreases due to low metabolic activity. This in turn leads to higher C contents since the turnover of prokaryotes in deeper depths becomes low enough for C to become assimilated.
How were the frequency numbers for four simultaneous mutations in shared genes determined for marine heterotrophs and marine autotrophs given an average mutation rate of 4 x 10-7 per DNA replication? (Provide an example of the calculation with units. Hint: cell and generation cancel out)
Frequency Number for 4 Simultaneous Mutations in Shared Genes:
Average Mutation Rate = 4 * 10-7 Per DNA Replication 365 / 16 = 22.8 Turnovers/Yr
(4 * 10-7)4 = 2.56 * 10-26 Mutations/Generation
3.6 * 1028 Cells * 22.8 = 8.2 * 1029 Cells/Yr * 2.56 * 10-26 Mutatations/Generation = 2.1 * 104 Mutations/Yr
Given the large population size and high mutation rate of prokaryotic cells, what are the implications with respect to genetic diversity and adaptive potential? Are point mutations the only way in which microbial genomes diversify and adapt?
Implications:No: Point mutations are not the only way in which microbial genomes diversify and adapt. There can also be HGT between other bacteria, different levels of gene regulation/expression, insertions/deletions, etc.
What relationships can be inferred between prokaryotic abundance, diversity, and metabolic potential based on the information provided in the text?
Relationships Between Prokaryotic Abundance, Diversity, and Metabolic Potential: High Prokaryotic Abundance <–> Higher Diversity <–> Higher Metabolic Potentials (More prokaryotes will lead to higher diversity via mutations and mutations could contribute to better genes that help with metabolism)
Discuss the role of microbial diversity and formation of coupled metabolism in driving global biogeochemical cycles.
What are the primary geophysical and biogeochemical processes that create and sustain conditions for life on Earth? How do abiotic versus biotic processes vary with respect to matter and energy transformation and how are they interconnected?
Primary Geophysical Processes = Tectonics and atmospheric photocehmical processes Primary Biogeochemical Processes = Microbially catalyzed, thermodynamically constrained redox reactions Abiotic vs. Biotic Processes vary with respect to matter/energy transformation and how are they interconnected: TODO
Why is Earth’s redox state considered an emergent property?
Earth’s Redox State = Emergent Property of Microbial Life on Planetary ScaleHow do reversible electron transfer reactions give rise to element and nutrient cycles at different ecological scales? What strategies do microbes use to overcome thermodynamic barriers to reversible electron flow?
Reversible electron transfer reactions –> Element + Nutrient Cycles at different ecological scales? TODO Strategies used by microbes to overcome thermodynamic barriers to reversible electron flow:Using information provided in the text, describe how the nitrogen cycle partitions between different redox “niches” and microbial groups. Is there a relationship between the nitrogen cycle and climate change?
N Cycle TODO
What is the relationship between microbial diversity and metabolic diversity and how does this relate to the discovery of new protein families from microbial community genomes?
Relationship between microbial diversity and metabolic diversity: Higher microbial diversity leads to higher metabolic diversity since different microbes may have a better chance of survival under different conditions using a different resource for metabolism (High metabolic diversity) Relation to discovery of new protein families from microbial community genomes: Microbial communities with high diversity (In terms of species and metabolic diversity) will have a higher chance of finding new protein families due to mutations creating more efficient or functionally different proteins in microbes.
On what basis do the authors consider microbes the guardians of metabolism?
Microbes = Guardians of MetabolismUtilize this space to include a bibliography of any literature you want associated with this module. We recommend keeping this as the final header under each module.
An example for Whitman and Wiebe (1998) has been included below.
Whitman WB, Coleman DC, and Wiebe WJ. 1998. Prokaryotes: The Unseen Majority. Proc Natl Acad Sci USA. 95(12):6578–6583. PMC33863
Falkowski PG, et al. 2009. The Microbial Engines That Drive Earth’s Biogeochemical Cycles. Science. 320(5879): 1034-1039. JSTOR20054782